Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Liu, Xi Peng ^a   Liu, Jian Hua ^a  

^a Shanghai Jiao Tong University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; AMINO ACID; COBALT; COPPER ION; CYTOSINE; DNA DIRECTED DNA POLYMERASE BETA; GUANINE; MANGANESE; NICKEL; OLIGONUCLEOTIDE; PHOSPHOROTHIOIC ACID; RECOMBINANT ENZYME; SODIUM CHLORIDE; THYMINE; URACIL; URACIL DNA GLYCOSIDASE; ZINC ION; DEOXYURIDINE; DIVALENT CATION; DNA DIRECTED DNA POLYMERASE; PFU DNA POLYMERASE;

AEROPYRUM PERNIX; ARTICLE; ENZYME ANALYSIS; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE TARGETING; NONHUMAN; PH MEASUREMENT; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION; PROTEIN FAMILY; TEMPERATURE MEASUREMENT; AEROPYRUM; DNA FRAGMENTATION; ENZYMOLOGY; GENETICS; METABOLISM; METHODOLOGY; PH; TEMPERATURE;

AEROPYRUM PERNIX;

AEROPYRUM; CATIONS, DIVALENT; DEOXYURIDINE; DNA FRAGMENTATION; DNA-DIRECTED DNA POLYMERASE; HYDROGEN-ION CONCENTRATION; POLYMERASE CHAIN REACTION; SODIUM CHLORIDE; TEMPERATURE; URACIL-DNA GLYCOSIDASE;

EID: 80555129565     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027248     Document Type: Article

References (39)

1. Lindahl T, Nyberg B, (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13: 3405-3410.
2. Hogrefe HH, Hansen CJ, Scott BR, Nielson KB, (2002) Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc Natl Acad Sci USA 99: 596-601.
3. Björnberg O, Neuhard J, Nyman PO, (2003) A bifunctional dCTP deaminase-dUTP nucleotidohydrolase from the hyperthermophilic archaeon Methanocaldococcus jannaschii. J Biol Chem 278: 20667-20672.
4. Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, et al. (2000) Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J Bacteriol 182: 1272-1279.
5. Sartori AA, Schär P, Fitz-Gibbon S, Miller JH, Jiricny J, (2001) Biochemical characterization of uracil processing activities in the hyperthermophilic archaeon Pyrobaculum aerophilum. J Biol Chem 276: 29979-29986.
6. Sartori AA, Fitz-Gibbon S, Yang H, Miller JH, Jiricny J, (2002) A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site. EMBO J 21: 3182-3191.
7. Shuttleworth G, Fogg MJ, Kurpiewski MR, Jen-Jacobson L, Connolly BA, (2004) Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. J Mol Biol 33: 7621-634.
8. Connolly BA, Fogg MJ, Shuttleworth G, Wilson BT, (2003) Uracil recognition by archaeal family B DNA polymerases. Biochem Soc Trans 31: 699-702.
9. Gill S, O'Neill R, Lewis RJ, Connolly BA, (2007) Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. J Mol Biol 372: 855-863.
10. Varshney U, Hutcheon T, van de Sande JH, (1988) Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung). J Biol Chem 263: 7776-7784.
11. Gallinari P, Jiricny J, (1996) A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383: 735-738.
12. Haushalter KA, Stukenberg PT, Kirschner MW, Verdine GL, (1999) Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors. Curr Biol 9: 174-185.
13. Lee HW, Dominy BN, Cao W, (2011) New Family of Deamination Repair Enzymes in Uracil-DNA Glycosylase Superfamily. J Biol Chem 286: 31282-31287.
14. Sakai T, Tokishita S, Mochizuki K, Motomiya A, Yamagata H, et al. (2008) Mutagenesis of uracil-DNA glycosylase deficient mutants of the extremely thermophilic eubacterium Thermus thermophilus. DNA Repair 7: 663-669.
15. Kaijalainen S, Karhunen PJ, Lalu K, Lindstom K, (1993) An alternative hot start technique for PCR in small volumes using beads of wax-embedded reaction components dried in trehalose. Nucleic Acids Res 21: 2959-2960.
16. Sharkey DJ, Scalice ER, Christy KG, Atwood SM, Daiss JL, (1994) Antibodies as thermolabile switches: high temperature triggering for the polymerase chain reaction. Biotechnology 12: 506-509.
17. Moretti T, Koons B, Budowle B, (1998) Enhancement of PCR amplification yield and specificity using AmpliTaq Gold DNA Polymerase. Biotechniques 25: 716-722.
18. Nilsson J, Bosnes M, Larsen F, Nygren PA, Uhlen M, et al. (1997) Heat-mediated activation of affinity-immobilized Taq DNA polymerase. Biotechniques 4: 744-751.
19. Kaboev OK, Luchkina LA, Tretiakov AN, Bahrmand AR, (2000) PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). Nucleic Acids Res 28: 94-102.
20. Kainz P, Schmiedlechner A, Strack HB, (2000) Specificity-enhanced hot-start PCR: addition of double-stranded DNA fragments adapted to the annealing temperature. Biotechniques 28: 278-282.
21. Dang C, Jayasena SD, (1996) Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. J Mol Biol 264: 268-278.
22. Barnes WM, Rowlyk KR, (2002) Magnesium precipitate hot start method for PCR. Mol Cell Probes 16: 167-171.
23. Kermekchiev MB, Tzekov A, Barnes WM, (2003) Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic Acids Res 31: 6139-6147.
24. Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, et al. (1999) Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res 6: 83-101, 145-152.
25. Liu XP, Li CP, Hou JL, Liu YF, Liang RB, et al. (2010) Expression and characterization of thymine-DNA glycosylase from Aeropyrum pernix. Protein Expr Purif 70: 1-6.
26. Parker JB, Stivers JT, (2008) Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions. Biochemistry 47: 8614-8622.
27. Greagg MA, Fogg MJ, Panayotou G, Evans SJ, Connolly BA, et al. (1999) A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc Natl Acad Sci U S A 96: 9045-9050.
28. Fogg MJ, Pearl LH, Connolly BA, (2002) Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat Struct Biol 9: 922-927.
29. Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, et al. (1991) High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108: 1-6.
30. Huang J, Lu J, Barany F, Cao W, (2001) Multiple cleavage activities of endonuclease V from Thermotoga maritima: recognition and strand nicking mechanism. Biochemistry 40: 8738-8748.
31. Hitchcock TM, Gao H, Cao W, (2004) Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V. Nucleic Acids Res 32: 4071-4080.
32. Mansfield C, Kerins SM, McCarthy TV, (2003) Characterisation of Archaeglobus fulgidus AlkA hypoxanthine DNA glycosylase activity. FEBS Lett 540: 171-175.
33. Emptage K, O'Neill R, Solovyova A, Connolly BA, (2008) Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. J Mol Biol 383: 762-771.
34. Kiyonari S, Uchimura M, Shirai T, Ishino Y, (2008) Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J Biol Chem 283: 24185-24193.
35. Kiyonari S, Tahara S, Shirai T, Iwai S, Ishino S, et al. (2009) Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. Nucleic Acids Res 37: 6439-6453.
36. Wang Y, Prosen DE, Mei L, Sullivan JC, Finney M, et al. (2004) A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Res 32: 1197-1207.
37. Michael M, Ingo K, Charles G, Eva L, Ulrike B, et al. (2002) Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes. J Biol Chem 277: 16179-16188.
38. Pavlov AR, Belova GI, Kozyavkin SA, Slesarev AI, (2002) Helix-hairpin-helix motifs confer salt resistance and processivity on chimeric DNA polymerases. Proc Natl Acad Sci USA 99: 13510-13515.
39. Davidson JF, Fox R, Harris DD, Lyons-Abbott S, Loeb LA, (2003) Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. Nucleic Acids Res 31: 4702-4709.